Henderson, 23, had not started a game for the Cobblers this season and had not featured in the matchday squad since November.
The former Norwich City youngster arrived at Sixfields in June 2007 but failed to score in 33 first-team appearances.
"Winger Ian Henderson has left Northampton Town after having his contract terminated," read a club statement.
"The decision means that he is free to find a new club when the transfer window opens in January."